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Phylogeny

  • 1.
    King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887
    Reference Link
  • 1.
    Cheng K, Burdine R, Dickinson M, Ekker S, Lin A, Lloyd K, Lutz C, MacRae C, Morrison J, O’Connor D, Postlethwait J, Rogers C, Sanchez S, Simpson J, Talbot W, Wallace D, Weimer J, Bellen H. Promoting validation and cross-phylogenetic integration in model organism research. Dis Model Mech. 2022;15(9). PMCID: PMC9531892
    Reference Link
  • 1.
    Lizewski R, Sealfon R, Park S, Smith G, Porter C, Gonzalez-Reiche A, Ge Y, Miller C, Goforth C, Pincas H, Termini M, Ramos I, Nair V, Lizewski S, Alshammary H, Cer R, Chen H, George M-C, Arnold C, Glang L, Long K, Malagon F, Marayag J, Nunez E, Rice G, Ana E, Schilling M, Smith D, Sugiharto V, Sun P, van de Guchte A, Khan Z, Dutta J, Vangeti S, Voegtly L, Weir D, Metcalf J, Troyanskaya O, Bishop-Lilly K, Grenfell B, van Bakel H, Letizia A, Sealfon S. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology. 2022;33(6):797–807. PMCID: PMC9531985
    Reference Link
  • 1.
    Yang D, Jones M, Naranjo S, Rideout W, Min K, Ho R, Wu W, Replogle J, Page J, Quinn J, Horns F, Qiu X, Chen M, Freed-Pastor W, McGinnis C, Patterson D, Gartner Z, Chow E, Bivona T, Chan M, Yosef N, Jacks T, Weissman J. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell. 2022;185(11):1905–1923.e25. PMCID: PMC9452598
    Reference Link
  • 1.
    Eickhoff M, Fei C, Cong J-P, Bassler B. LuxT Is a Global Regulator of Low-Cell-Density Behaviors, Including Type III Secretion, Siderophore Production, and Aerolysin Production, in Vibrio harveyi. mBio. 2022;13(1):e0362121. PMCID: PMC8764538
    Reference Link
  • 1.
    King S, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021;17(11):e1009560. PMCID: PMC8601562
    Reference Link
  • 1.
    Behnke M, Khan A, Lauron E, Jimah J, Wang Q, Tolia N, Sibley D. Rhoptry Proteins ROP5 and ROP18 Are Major Murine Virulence Factors in Genetically Divergent South American Strains of Toxoplasma gondii. PLoS Genet. 2015;11(8):e1005434. PMCID: PMC4546408
    Reference Link
  • 1.
    Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics. 2021;37(Suppl_1):i133-i141. PMCID: PMC8275333
    Reference Link
  • 1.
    Eickhoff M, Fei C, Huang X, Bassler B. LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA. PLoS Genet. 2021;17(4):e1009336. PMCID: PMC8043402
    Reference Link
  • 1.
    Letizia A, Ramos I, Obla A, Goforth C, Weir D, Ge Y, Bamman M, Dutta J, Ellis E, Estrella L, George M-C, Gonzalez-Reiche A, Graham W, van de Guchte A, Gutierrez R, Jones F, Kalomoiri A, Lizewski R, Lizewski S, Marayag J, Marjanovic N, Millar E, Nair V, Nudelman G, Nunez E, Pike B, Porter C, Regeimbal J, Rirak S, Ana E, Sealfon R, Sebra R, Simons M, Soares-Schanoski A, Sugiharto V, Termini M, Vangeti S, Williams C, Troyanskaya O, van Bakel H, Sealfon S. SARS-CoV-2 Transmission among Marine Recruits during Quarantine. N Engl J Med. 2020;383(25):2407–2416. PMCID: PMC7675690
    Reference Link
  • 1.
    Doane M, Morris M, Papudeshi B, Allen L, Pande D, Haggerty J, Johri S, Turnlund A, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery A, Lima L, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards R, Dinsdale E. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome. 2020;8(1):93. PMCID: PMC7293782
    Reference Link
  • 1.
    Moore G, Gitai Z. Both clinical and environmental Caulobacter species are virulent in the Galleria mellonella infection model. PLoS One. 2020;15(3):e0230006. PMCID: PMC7067423
    Reference Link
  • 1.
    Aardema M, vonHoldt B, Fritz M, Davis S. Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes. Parasit Vectors. 2020;13(1):8. PMCID: PMC6950815
    Reference Link
  • 1.
    Tianero M, Balaich J, Donia M. Localized production of defence chemicals by intracellular symbionts of Haliclona sponges. Nat Microbiol. 2019;4(7):1149–1159. PMCID: PMC8647704
    Reference Link
  • 1.
    Wang R, Seyedsayamdost M. Roseochelin B, an Algaecidal Natural Product Synthesized by the Roseobacter Phaeobacter inhibens in Response to Algal Sinapic Acid. Org Lett. 2017;19(19):5138–5141. PMID: 28920692
    Reference Link
  • 1.
    Charruau P, Johnston R, Stahler D, Lea A, Snyder-Mackler N, Smith D, vonHoldt B, Cole S, Tung J, Wayne R. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol. 2016;33(8):1967–78. PMCID: PMC5854094
    Reference Link
  • 1.
    McCulloch K, Yuan F, Zhen Y, Aardema M, Smith G, Llorente-Bousquets J, Andolfatto P, Briscoe A. Sexual Dimorphism and Retinal Mosaic Diversification following the Evolution of a Violet Receptor in Butterflies. Mol Biol Evol. 2017;34(9):2271–2284. PMID: 28505307
    Reference Link
  • 1.
    Guo C-J, Chang F-Y, Wyche T, Backus K, Acker T, Funabashi M, Taketani M, Donia M, Nayfach S, Pollard K, Craik C, Cravatt B, Clardy J, Voigt C, Fischbach M. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017;168(3):517–526.e18. PMCID: PMC5302092
    Reference Link
  • 1.
    Inclan Y, Persat A, Greninger A, Von Dollen J, Johnson J, Krogan N, Gitai Z, Engel J. A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa. Mol Microbiol. 2016;101(4):590–605. PMCID: PMC4980298
    Reference Link
  • 1.
    Aardema M, Andolfatto P. Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies. Evolution. 2016;70(8):1913–21. PMCID: PMC4980202
    Reference Link
  • 1.
    vonHoldt B, Takuno S, Gaut B. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012;29(10):3193–203. PMID: 22593226
    Reference Link
  • 1.
    Nadimpalli S, Persikov A, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015;11(3):e1005011. PMCID: PMC4351887
    Reference Link
  • 1.
    Jenni S, Goyal Y, von Grotthuss M, Shvartsman S, Klein D. Structural Basis of Neurohormone Perception by the Receptor Tyrosine Kinase Torso. Mol Cell. 2015;60(6):941–52. PMID: 26698662
    Reference Link
  • 1.
    Brown J, McBride C, Johnson P, Ritchie S, Paupy C, Bossin H, Lutomiah J, Fernandez-Salas I, Ponlawat A, Cornel A, Black W, Gorrochotegui-Escalante N, Urdaneta-Marquez L, Sylla M, Slotman M, Murray K, Walker C, Powell J. Worldwide patterns of genetic differentiation imply multiple ’domestications’ of Aedes aegypti, a major vector of human diseases. Proc Biol Sci. 2011;278(1717):2446–54. PMCID: PMC3125627
    Reference Link
  • 1.
    Matthews B, McBride C, DeGennaro M, Despo O, Vosshall L. The neurotranscriptome of the Aedes aegypti mosquito. BMC Genomics. 2016;17:32. PMCID: PMC4704297
    Reference Link
  • 1.
    Schumer M, Cui R, Powell D, Rosenthal G, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol. 2016;25(11):2661–79. PMID: 26937625
    Reference Link
  • 1.
    Kwan J, Tianero M, Donia M, Wyche T, Bugni T, Schmidt E. Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella. PLoS One. 2014;9(5):e95850. PMCID: PMC4008419
    Reference Link
  • 1.
    Williams B, Van Benschoten A, Cimermancic P, Donia M, Zimmermann M, Taketani M, Ishihara A, Kashyap P, Fraser J, Fischbach M. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014;16(4):495–503. PMCID: PMC4260654
    Reference Link

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